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Maximum 65,536 rows and 256 columns.
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936
Todo
Skyline
Thermo Eclipse and Fusion Lumos method export
Kaipo Tamura
3
resolved
23.1
935
Defect
Skyline
Capture injection time as sample-scoped chromatogram
Brendan MacLean
3
open
934
Todo
Skyline
Enable optimization method export for more TOF instruments
Kaipo Tamura
2
open
933
Todo
Skyline
Thorium method export
Kaipo Tamura
2
open
932
Todo
TestResults
Summarize/graph pass1 iteration count for tests
Kaipo Tamura
4
open
931
Todo
Skyline
Agilent MH 12 method export
Kaipo Tamura
2
open
930
Todo
Skyline
Export isolation list (DIA) for Bruker timsTOF
Kaipo Tamura
4
open
929
Defect
Skyline
When explicit ion mobility values are used, the reported CCS value should be adjusted appropriately in the resulting chromatogram extractions
Brian Pratt
3
open
928
Defect
Skyline
AssumptionException saving document with protein groups sometimes
Guest
2
closed
23.1
927
Defect
Skyline
Bibliospec - retain fragment charge values in MGF files
Brian Pratt
3
open
926
Todo
Skyline
Implement Bruker Paser support in BlibBuild
Matt Chambers
2
open
23.1
925
Defect
Skyline
Targets view hangs during mouse-over with peptides longer than 2000 or so
Nick Shulman
3
open
924
Defect
Skyline
Fix ability to provide a protein description in Edit > Insert > Peptides
Nick Shulman
3
open
923
Todo
Skyline
Implement an interface that allows for multiple algorithms to do peak group assignment
Nick Shulman
3
open
922
Defect
Skyline
Edit > Find needs to use LongWaitDlg and support cancel
Nick Shulman
3
open
23.1
921
Todo
Skyline
Transition list reader should identify special ions by m/z the same way it does calculated peptide fragment ions
Brian Pratt
3
open
920
Defect
Skyline
When Group By fails in replicate comparison graphs you lose the Order By menu item
Nick Shulman
3
open
23.1
919
Defect
Skyline
SpectrumLibraryInfoDlg scoring columns should match library build columns
Brendan MacLean
3
resolved
23.1
918
Defect
Skyline
a few issues with "Use Results" in ion mobility libraries
Brian Pratt
3
open
23.1
917
Defect
Skyline
Ion mobility high energy offset should be applied for all Full Scan MS/MS modes, not just All Ions DIA
Guest
3
closed
23.1
916
Documentation
Skyline
Document normalization methods
Nick Shulman
2
open
22.2
915
Defect
Skyline
Library Match and Full-Scan - Right-click menu item order is broken in 22.2
Rita Chupalov
2
open
22.2
914
Defect
Skyline
Proteomics features still showing in small molecule mode
Brian Pratt
3
open
23.1
913
Todo
Skyline
Make Ctrl-A work in Import > Results form to select all files in a folder
Brendan MacLean
3
open
22.2
912
Defect
Skyline
Auto-Zoom X Axis > Best Peak does nothing for chromatograms with removed peaks
Kaipo Tamura
3
open
23.1
911
Defect
Skyline
Calibration Curve graph calculates concentrations on double-blanks (NaN or infinity)
Nick Shulman
3
open
23.1
910
Defect
Skyline
Synchonized integration has trouble with removed peaks
Brendan MacLean
3
resolved
23.1
909
Defect
Skyline
Red dots for dotp values below the cut-off appear behind bars
Rita Chupalov
3
open
23.1
908
Todo
Skyline
Command Line Enhancement Request : Include MS/MS Filtering Options
Brian Pratt
3
open
23.1
907
Defect
Skyline
ViewLibraryDlg right-click menu lagging behind Library Match right-click menu
Rita Chupalov
2
open
23.1
906
Defect
Skyline
A few details working with Bruker PASER assay library lists
Brian Pratt
3
open
22.2
905
Defect
Skyline
IndexOutOfRangeException bringing up GraphFullScan immediately after modifying the document
Rita Chupalov
3
open
23.1
904
Defect
Skyline
Store more spectrum and instrument information in .blib files when possible
Matt Chambers
2
open
23.1
903
Defect
Skyline
Show names of default settings, and save settings with document when exporting a transition list
Kaipo Tamura
3
open
22.2
902
Todo
Skyline
add an ion mobility range filter in Transition Settings IM tab similar to instrument settings tab's mz range filter
Brian Pratt
3
open
901
Defect
Skyline
Newly added annotations don't show up in the Rule Editor
Nick Shulman
3
open
22.2
900
Defect
Skyline
Opening a .skyp file shows no progress until the file is downloaded
Vagisha Sharma
3
open
22.2
899
Todo
Skyline
Adding targets from DDA library seems useful to be able to specify a number of runs a peptide got ID'd in
Matt Chambers
3
open
23.1
898
Defect
Skyline
Record the Document Grid selection in the Undo/Redo buffer during Document Grid editing events
Brendan MacLean
3
resolved
22.2
897
Todo
Skyline
Make Ctrl-Z (Undo) and Ctrl-Y (Redo) work in Document Grid
Brendan MacLean
2
resolved
22.2
896
Defect
Skyline
IMS library "Use Results" should ignore poor quality chromatographic peaks
Brian Pratt
3
open
895
Todo
Skyline
"Split Graphs" equivalent (stacked MS1 and MS/MS views) for Full Scan view
Brian Pratt
3
open
894
Todo
Skyline
Make "Use Results" isolation scheme work for Import > Peptide Search of DIA
Kaipo Tamura
2
open
22.2
893
Todo
Skyline
Need a way to turn off switching replicates in retention times - regression plot
Rita Chupalov
3
open
22.1
892
Defect
Skyline
Export > Transition / Isolation List with scheduling seems broken for counting multiple methods
Guest
1
closed
21.2
891
Defect
Skyline
Adjusting peak boundaries with non-quantitative transitions is confusing
Nick Shulman
3
open
22.2
890
Defect
Skyline
Audit log Skyline Version upgrade
Kaipo Tamura
3
open
22.1
889
Todo
Skyline
Make more instrument parameters available on Files in the Document Grid
Matt Chambers
3
open
22.1
888
Defect
Skyline
File > Import > Peptide Search with existing library reports the build settings in the Audit Log
Brendan MacLean
2
resolved
22.2
887
Defect
Skyline
Smooth handling of .skyp file for server lacking credentials
Vagisha Sharma
3
open
22.1
886
Defect
Skyline
AutoQC Loader stops scrolling log text area after a wrapped line
Vagisha Sharma
3
open
22.1
885
Defect
Skyline
Dotp line graph points should be clickable for changing the active replicate
Rita Chupalov
3
open
22.1
884
Defect
Skyline
Some user are really unhappy that they can't type transition lists into Skyline like they used to do
Brian Pratt
3
open
883
Documentation
Skyline
Update tutorials with new library building interface
Guest
2
closed
882
Todo
Skyline
Clean out apparent IMS related cruft in Full Scan tab
Guest
3
closed
881
Defect
Skyline
Move Bruker timsTOF method export into BuildMethod
Kaipo Tamura
3
open
880
Todo
Skyline
SSL format changes for Feature Detection
Brian Pratt
3
open
22.1
879
Defect
Skyline
Need some way to show user FAIMS information in raw scan view, to demystify jagged chromatograms before IM filters are applied
Brian Pratt
3
open
878
Defect
Skyline
Need to handle retention time shifts for deuterated internal standards
Brian Pratt
3
open
877
Defect
Skyline
"How Skyline Calculates Peak Areas and Heights" tip could use updating
Brendan MacLean
3
open
876
Defect
Skyline
Typo in "Skyline Small Molecule Method Development and CE Optimization" tutorial
Nat Brace
3
open
875
Defect
Skyline
The adduct pick list (as used in Modify... in Targets tree) should include [M+] and [M-]
Guest
3
closed
874
Defect
Skyline
Default Win32 MAX_PATH value of 260 is too small for some users
Brian Pratt
3
open
873
Defect
Skyline
Feature request: single molecule/peptide re-integration
Brendan MacLean
3
open
872
Defect
Skyline
Document created by an m/z-only transition list should not depend on list order
Guest
3
closed
22.1
871
Defect
Skyline
Clean up the interaction of small molecule transition list imports and Transition Settings that affect precursor isotope ([M+1], [M+2] etc) creation
Brian Pratt
1
open
22.1
870
Todo
Skyline
Implement special peak statistics for DDA MS/MS
Guest
1
closed
22.2
869
Todo
Skyline
Add a Prosit RT calculator parallel to SSRCalc
Kaipo Tamura
3
open
868
Todo
Skyline
Consider generating a dictionary of less common isotopes instead of hardcoding them piecemeal in response to user requests
Brian Pratt
3
open
867
Todo
Skyline
Possible Improvements to Edit>Insert>TransitionList
Brian Pratt
3
open
22.1
866
Defect
Skyline
Provide option in Skyline to upload a minimized library to Panorama
Guest
3
closed
22.1
865
Defect
Skyline
Adding heavy mods in Peptide Settings does not add "Ratio to Heavy" normalization to Quantification tab
Guest
1
closed
21.2
864
Defect
Skyline
Various issues reading this small molecule transition list with heavy label formulas
Guest
3
closed
22.1
863
Defect
Skyline
Problem loading a small mol document with isotope labels - Skyline complains that they aren't known modifications (which should not matter)
Guest
3
closed
22.1
862
Defect
Skyline
"Importing Results..." window should resize its multi-file progress control when there's a vertical scrollbar in use (currently cuts off the "Cancel" buttons and looks funny)
Guest
3
closed
22.1
861
Todo
Skyline
Implement better peptide to protein assignment strategies for target selection
Matt Chambers
2
open
22.1
860
Defect
Skyline
Support more than one fragment specification per line in transition list column picker, for small molecules at least
Brian Pratt
3
open
859
Defect
Skyline
Add peak apex CCS to Transition Result
Nick Shulman
3
open
22.1
858
Defect
Skyline
make "ImportPeptideSearch with the IMS filtering visible" a form view that can be shown in the SkylineTester Forms tab
Guest
3
closed
22.1
857
Defect
Skyline
ImportTransitionListColumnSelectDlg lags a bit when associate proteins checked
Brendan MacLean
3
resolved
21.2
856
Defect
Skyline
When training a "Default" peak scoring model, the model should be able to use feature scores that are present for some but not all peptides
Guest
3
closed
22.1
855
Defect
Skyline
Log scale with median normalization does not mention the normalization in the y-axis label
Brendan MacLean
3
resolved
22.2
854
Defect
Skyline
Peak Areas - Replicate Comparison - Normalize to strangely chooses poorly
Brendan MacLean
2
resolved
21.2
853
Defect
Skyline
Remove peak should make dotp annotations and line missing
Guest
1
closed
21.2
852
Defect
Skyline
Full-Scan graph no longer auto-scales the y-axis when clicking arrow buttons
Brendan MacLean
2
resolved
21.2
851
Todo
Skyline
Rename auto trained peak scoring models
Kaipo Tamura
3
open
22.1
850
Defect
Skyline
Fix performance issue with ion moblity filtering in library viewer
Brian Pratt
3
open
22.1
849
Defect
Skyline
Failure opening .sky file saying audit log entry has been modified
Brendan MacLean
2
resolved
21.2
848
Defect
Skyline
Show a better error message if check for Panorama server fails
Vagisha Sharma
1
open
23.1
847
Defect
Skyline
Add option to use explicit RT instead of measured for exporting scheduled methods
Kaipo Tamura
3
open
846
Defect
Skyline
Trouble exporting polarity-switching QQQ method from Skyline to Agilent-6495C
Kaipo Tamura
3
open
845
Defect
Skyline
User says Agilent 6495C can go down to a dwell time of 0.5ms, but we insist on integer dwell times in UI
Kaipo Tamura
3
open
844
Defect
Skyline
Libraries should load without error even if the directory that the library is in is not writeable.
Guest
2
closed
21.2
843
Defect
Skyline
Update "_elementMasses" in MaxQuantReader.cpp
Guest
2
closed
21.2
842
Todo
Skyline
Add a setting for RT annotation display to Chromatogram graph right-click > properties form
Guest
2
closed
841
Defect
Skyline
Insert Transition List with heavy precursors results in document that cannot be opened.
Guest
2
closed
840
Defect
Skyline
is M+Na precursor being handled properly in display of split graphs and heat maps, and is it being used properly in SONAR extraction?
Guest
3
closed
839
Defect
Skyline
Inconsistent representation of "squared" in IM peak display on chromatogram graphs
Guest
3
closed
838
Defect
Skyline
initial zoom on ion mobility heat map should not default to zero as lower range
Guest
3
closed
21.1
837
Defect
Skyline
Import Peptide wizard "Configure Full-Scan Settings" IMS stuff should have its own page/step
Guest
3
closed
21.1